Alloplasmic wheat, Triticum aestivum cv. Norin 26 with Aegilops crassa cytoplasm, shows photoperiod-sensitive cytoplasmic male sterility (PCMS). This alloplasmic line expresses pistillody of anthers only when grown in the long-day condition (>15 h light). To assess molecular basis of the PCMS system, we carried out Southern and Northern blot analyzes by using the mitochondrial DNAs and RNAs isolated from seedlings of alloplasmic lines showing various phenotypes for PCMS and probing them with twelve mitochondrial genes. All RFLP patterns of mitochondrial DNA from alloplasmic lines greatly differed from those of common wheat, and were slightly changed from those of their parental species, i.e., Ae.crassa. This indicates that nuclear substitutions between the related plant species induce the structural alterations of the mitochondrial genome. Furthermore, RFLP patterns of (cr)-N61 and FR-mutant probed with cox III and orf25 were identical with each other, but different from those of the other alloplasmic lines, indicating the nuclei of N61 and FR-mutant harbor some gene (s) that induces the structural alterations of the mitochondrial genome around the regions of coxIII and orf25 genes. The transcription patterns of atp6 and cob in Ae.crassa type were different from those of T.aestivum type. Furthermore, the orf25 transcript of alloplasmic wheats was about 300 nucleotides longer than that of euplasmic lines including the Ae.crassa pure line, suggesting that transcription patterns of orf25 are associated with the recovery from the PCMS phenomenon. These data clearly show the mutual cross-talk between the nuclear genome and chondriome. These observations raise the possibility that the dysfunction of mitochondria caused by the failure of a cooperative control of mitochondrial gene (s) expression influences the pathway of flower morphogenesis, especially in the organ identity step.